Vannutelli Anaïs, Perreault Jean-Pierre, Ouangraoua Aïda
Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada.
NAR Genom Bioinform. 2022 Mar 4;4(1):lqac010. doi: 10.1093/nargab/lqac010. eCollection 2022 Mar.
G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in humans and a few other species. Recently, predictions have been made with bacterial and archaeal genomes. Nevertheless, a global comparison of predicted G4s (pG4s) across and within the three living kingdoms has not been addressed. In this study, we aimed to predict G4s in genes and transcripts of all kingdoms of living organisms and investigated the differences in their distributions. The relation of the predictions with GC content was studied. It appears that GC content is not the only parameter impacting G4 predictions and abundance. The distribution of pG4 densities varies depending on the class of transcripts and the group of species. Indeed, we have observed that, in coding transcripts, there are more predicted G4s than expected for eukaryotes but not for archaea and bacteria, while in noncoding transcripts, there are as many or fewer predicted G4s in all species groups. We even noticed that some species with the same GC content presented different pG4 profiles. For instance, and both have 60% of GC content, but the former has a pG4 density of 0.07 and the latter 1.16.
G-四链体是在DNA和RNA中发现的基序，可折叠成三级结构。到目前为止，它们主要在人类和其他一些物种中进行了实验研究。最近，人们对细菌和古细菌基因组进行了预测。然而，尚未对三个生物界之间和内部预测的G4（pG4）进行全局比较。在本研究中，我们旨在预测所有生物界的基因和转录本中的G4，并研究它们分布的差异。研究了预测结果与GC含量的关系。看来GC含量不是影响G4预测和丰度的唯一参数。pG4密度的分布因转录本类别和物种组而异。实际上，我们观察到，在编码转录本中，真核生物预测的G4比预期的多，但古细菌和细菌并非如此，而在非编码转录本中，所有物种组预测的G4数量相同或更少。我们甚至注意到，一些具有相同GC含量的物种呈现出不同的pG4谱。例如，[此处原文缺失具体物种名1]和[此处原文缺失具体物种名2]的GC含量均为60%，但前者的pG4密度为0.07，后者为1.16。
